Project 4: Application of Comparative Genomics, Transcriptomics, & Proteomics Opt

项目4：比较基因组学、转录组学的应用，

• 批准号: 7792406
• 负责人: Lisa Alvarez-Cohen
• 金额: $ 43.49万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7792406
• 关键词: Address; Advanced Development; Bacteria; Bioremediations; Chemicals; Communities; Complex; Data; Drug Metabolic Detoxication; Environment; Ethylenes; Exposure to; Funding; Gene Expression; Gene Expression Profile; Genes; Genome; Genomics; Goals; Growth; Health; Human; In Situ; Kinetics; Laboratories; Length; Location; Mass Spectrum Analysis; Measures; Metabolic; Metabolic Pathway; Metabolism; Methodology; Microbe; Modeling; Molecular; Nitrogen; Nutrient; Nutritional; Organism; Oxidation-Reduction; Pathway interactions; Physiological; Poison; Process; Production; Proteins; Proteomics; Regulator Genes; Research; Role; Sampling; Signal Transduction; Site; Solvents; Stimulus; Superfund; Surface; Technology; Testing; Time; Toxic effect; Trichloroethylene; Trypsin; Vitamin B 12; Work; base; cold temperature; comparative; dechlorination; dehalogenation; electron donor; exposed human population; gene interaction; improved; insight; meetings; microbial; microbial community; pollutant; protein expression; research study; response; superfund site; tool; transcriptomics

This proposal will apply advanced molecular tools to understand and optimize the microbial detoxification of common Superfund pollutants, perchloroethene (PCE) and trichloroethene (TCE), which pose a significant threat to human and ecological health. By studying the fundamental processes responsible for anaerobic microbial degradation of PCE and TCE, this work will promote improved situ bioremediation processes. Previous NIEHS-funded research sought to identify and understand the microbes within complex communities responsible for dechlorination. This work takes the next logical step by focusing on the only genus of bacteria, Dehalococcoides, known to completely reduce PCE and TCE to ethene. Whole-genome microarrays, proteomic analyses, and quantitative PCR will be used to characterize the genomic differences between a variety of Dehalococcoides strains and to evaluate gene expression and proteomic changes caused by reductive dechlorination of a variety of substrates, growth in simple and complex microbial communities, and other physiological perturbations. Genomic and transcriptomic comparison of Dehalococcoides strains with different degradation abilities will identify the pathways responsible for specific and general metabolism as well as reveal the evolutionary relationship between the various isolated strains. Transcriptomic comparison of Dehalococcoides strains in pure and mixed cultures will identify pathways involved in inter-species interactions, reveal the nutritional needs and metabolic roles of Dehalococcoides in consortia, and address the limitation in bioremediation applications presented by the poor growth of isolated Dehalococcoides strains. Data from strain identification, gene.expression, and protein production will be complied into kinetic models that can be used to predict rates of reductive dechlorination by poorly characterized microbial communities. This research will meet the SBRP goal of limiting the human exposure and toxicity of chemicals commonly found at Superfund sites by advancing the development of in situ bioremediation of PCE and TCE, a technology that destroys contaminants in their subsurface location without extraction to the surface, avoiding potential human and ecological exposure.

该提案将应用先进的分子工具来了解和优化微生物 超巨额基金常见污染物四氯乙烯和三氯乙烯的解毒， 对人类和生态健康构成重大威胁。通过研究基本过程 负责厌氧微生物降解PCE和TCE，这项工作将促进改善现场 生物修复过程。以前NIEHS资助的研究试图识别和理解 负责脱氯的复杂群落中的微生物。这项工作采取了下一个合乎逻辑的步骤 通过专注于唯一的细菌属，Dehalococcoides，已知完全减少PCE和TCE， 乙烯。全基因组微阵列、蛋白质组学分析和定量PCR将用于表征 各种Dehalococcoides菌株之间的基因组差异，并评估基因表达 和蛋白质组的变化所造成的还原脱氯的各种底物，生长在简单的， 复杂的微生物群落和其他生理扰动。基因组和转录组 比较具有不同降解能力的Dehalococcoides菌株将确定降解途径 负责特定和一般代谢，以及揭示进化之间的关系， 各种分离的菌株。纯培养和混合培养中脱卤球菌属菌株的转录组学比较 将确定参与物种间相互作用的途径，揭示营养需求和代谢作用 的Dehalococcoides在财团，并解决生物修复应用的局限性提出的 分离的Dehalococcoides菌株生长不良。来自菌株鉴定、基因表达和 蛋白质生产将被编译成动力学模型，可用于预测还原速率。 微生物群落特性不佳导致的脱氯。这项研究将满足SBRP的目标， 限制人类接触和毒性的化学品通常发现在超级基金的网站， PCE和TCE的原位生物修复技术的发展，这是一种破坏其 地下位置，无需提取到表面，避免潜在的人类和生态暴露。